LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -39.007040 0.0000000) to (22.520725 39.007040 6.3277775) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9265066 5.4746723 6.3277775 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.007040 0.0000000) to (22.520725 39.007040 6.3277775) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9265066 5.4746723 6.3277775 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.007040 0.0000000) to (22.520725 39.007040 6.3277775) create_atoms CPU = 0.001 seconds 458 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 18 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_673777079812_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.412 | 5.412 | 5.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2708.8108 0 -2708.8108 45961.727 76 0 -2965.0202 0 -2965.0202 1909.251 Loop time of 0.938825 on 1 procs for 76 steps with 912 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2708.81083279236 -2965.01744957831 -2965.02018220533 Force two-norm initial, final = 367.71838 0.20298884 Force max component initial, final = 105.32430 0.018468514 Final line search alpha, max atom move = 1.0000000 0.018468514 Iterations, force evaluations = 76 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89672 | 0.89672 | 0.89672 | 0.0 | 95.51 Neigh | 0.025946 | 0.025946 | 0.025946 | 0.0 | 2.76 Comm | 0.0090012 | 0.0090012 | 0.0090012 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007162 | | | 0.76 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6832.00 ave 6832 max 6832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204932.0 ave 204932 max 204932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204932 Ave neighs/atom = 224.70614 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.407 | 5.407 | 5.407 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -2965.0202 0 -2965.0202 1909.251 11117.485 80 0 -2965.1105 0 -2965.1105 107.01472 11132.192 Loop time of 0.0396734 on 1 procs for 4 steps with 912 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2965.02018220534 -2965.10938732353 -2965.11054059092 Force two-norm initial, final = 48.626283 1.3736229 Force max component initial, final = 45.733553 1.0034825 Final line search alpha, max atom move = 0.00022417775 0.00022495844 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038191 | 0.038191 | 0.038191 | 0.0 | 96.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028894 | 0.00028894 | 0.00028894 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001193 | | | 3.01 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6403.00 ave 6403 max 6403 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205080.0 ave 205080 max 205080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205080 Ave neighs/atom = 224.86842 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.545 | 5.545 | 5.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2965.1105 0 -2965.1105 107.01472 Loop time of 1.684e-06 on 1 procs for 0 steps with 912 atoms 178.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.684e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6383.00 ave 6383 max 6383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205144.0 ave 205144 max 205144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205144 Ave neighs/atom = 224.93860 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.545 | 5.545 | 5.545 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2965.1105 -2965.1105 22.593413 77.854386 6.3287184 107.01472 107.01472 144.89017 75.969045 100.18496 2.3482447 678.87502 Loop time of 2.012e-06 on 1 procs for 0 steps with 912 atoms 149.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.012e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6383.00 ave 6383 max 6383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102572.0 ave 102572 max 102572 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205144.0 ave 205144 max 205144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205144 Ave neighs/atom = 224.93860 Neighbor list builds = 0 Dangerous builds = 0 912 -2965.11054059092 eV 2.34824467170159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01